Diffraction quality

Once preliminary crystallizing conditions have been found, they usually have to be optimized to grow large, diffraction quality crystals. There are several methods that are commonly used for improving the conditions. Diffraction quality crystals can only be judged by diffraction experiments, and the requirements will vary depending on what is required. 

At Oak Ridge, the focus was to develop specific-sequence DNA to improve the diffraction quality of NCP crystals. The positioning of the DNA on the histone core has to be precise so that all the NCPs are identical. A project was undertaken to understand the DNA sequence effects on nucleosome phasing [25]. Second, a DNA palindrome was developed to extend the two-fold symmetry of the histone core to the DNA. The objective was to eliminate the two-fold disorder caused by the indeterminacy of packing of an asymmetric particle into the crystal lattice. A palindrome based on one-half of the primary candidate sequence was constructed and methods were developed to produce the palindrome fragment in large quantities for reconstitution of NCPs. 

Given the nascent nature of these software tools, SGX developed its own method to evaluate or score the diffraction quality. The SGX system is based on two established software programs, d TREK (Pflugrath, 1999) and Mosflm (Leslie, 1992). These programs index diffraction images to determine the appropriate Laue group. In addition, they provide an analysis of the properties of the... 

Bamford, J. K., et al. (2002). Diffraction quality crystals of PRDl, a 66-MDa dsDNA virus with an internal membrane. /. Struct. Biol. 139,103-112. 

Chaven, N. E., and Saridakis, E. 2008. Protein crystallization From purified protein to diffraction-quality crystal. Nat Meth. 5 147-53. 

Evidence for the weak hydrogen bond nature of C—H it interactions has been reported recently by Madhavi et al. in a study of the complexes of 2,3,7,8-tetraphenyl-l,9,10-anthyridine 26 with toluene and chlorobenzene [56]. It was found that diffraction quality crystals of 26 could not readily be obtained from common solvents, with the exception of toluene, which produced a 1 1 solvate,... 

As the use of low-temperature techniques becomes more routine, the quality of the analyses in this regard should improve, but this will be affected by a trend toward the study of more complex molecules where the diffraction quality of the crystals and the observation-to-parameter ratio becomes less favorable for locating the hydrogen atoms. 

The diffraction qualities of the crystals with A-, B-, and Z-DNA differ, and therefore the results obtained are difficult to compare. Crystals of Z-DNA, in general, diffract to 1.2 A resolution or better, whereas in A- and B-DNA, diffrac-... 

Each interface contains 11 or 12 hydrogen bonds or salt bridge interactions. Although the GH/GHR complex buries more surface area into its interface, it stiU contains only 12 specific interactions. Three of the IFN-7/ IFN-7RI interactions occur between mainchain atoms in the AB loop of IFN-7 and the L2 loop of IFN-7RI. In addition to the 12 receptor-cytokine interactions, seven water molecules bridge the donor and acceptor groups of IFN-7 and IFN-7RI via hydrogen bonds (Randal and Kossiakoff, 2001). Since the B-factors for the water and protein atoms in the complex are essentially the same, the water molecules are considered to be an integral part of the interface. The presence of ordered water molecules in the IFN-7/IFN-7RI interface is not likely unique, since the IL-lO/IL-lORl interface is even more polar. However, the poorer diffraction quality of IL-10 complex crystals ( 2.9A versus 2.0A) obtained at this time prevents a detailed description of the interfacial waters. The water molecules in the... 

The first diprotonated sapphyrin-derived anion complex, a fluoride-containing chelate [15], was obtained in quite an unusual fashion. During an attempt to obtain an X-ray diffraction quality crystal of the diprotonated sapphyrin 216,... 

Unfortunately, crystals of X-ray diffraction quality for the above cobalt and zinc derivatives could not be obtained. Thus, tentative assignments of structure were made on the basis of mass spectrometric analysis. Such studies were consistent with the apparent complexation of only one metal atom by the sapphyrin core. They also revealed a parent ion for each of these complexes that was considered most in accord with the symmetrical structures represented by 5,83 and 5.84 (Figure 5.5.1). In other words, based on these analyses. Woodward and coworkers proposed cobalt(II) and zinc(II) sapphyrin complexes wherein only four of the five possible nitrogen centers interacted with the metal center, and only two of the three possible NH protons became lost upon complexation. ... 

The chemist or biochemist who wants to determine the crystal structure of a molecule must first obtain diffraction-quality crystals. In this chapter we will describe some of the general methods commonly used for obtaining crystals and what can be learned from their unit cells. 

Proteins generally are available in small quantities and are often difficult to crystallize. Therefore the strategy is to use a combinatorial method in which selected combinations of different organic solvents, different pH ranges, different salt concentrations, and different precipitating agents are tested for their ability to aid in production of diffraction-quality crystals. Very small amounts of protein solution (10-30 mg/ml), for example, 2 pi (also sometimes called 2 A) are used. In this way the best conditions for crystallization can be refined. Recipes for growing crystals are usually only specific for a particular protein. 

Single-component solvent evaporation methods depend on the removal of solvent in order to obtain the saturated solution required for crystallization to occur. If single-solvent solutions do not yield diffraction-quality crystals, mixtures of solvents may be tried. Multi-component solvent evaporation methods depend on the difference in the... 

It is, however, not always easy to grow crystals. When crystals of a chosen compound defy the best efforts of the crystallographer to grow them, it is sometimes possible to prepare molecular complexes that crystallize more readily, where one component of the complex is the compound of interest. An example is provided by Margaret Etter and coworkers. They demonstrated that, if a compound contains an acidic hydrogen atom that can readily form hydrogen bonds, then formation of a complex with triphenylphosphine oxide may lead to diffraction-quality crystals of the complex. 

The crystal should be single, of good diffracting quality, and approximately equidimensional. It is mounted on a gl2iss fiber or, if unstable, in a glass capillary. 

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